def testGetPairsNoLandmarksNoTrigPoints(self):
"""
If a scanned read has no landmarks or trig points, its getPairs
method should generate no pairs.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
self.assertEqual([], list(read.getPairs()))
def testNoCoverage(self):
"""
If a scanned read has no landmarks or trig points, its coveredIndices
method must return the empty set.
"""
read = ScannedRead(AARead('id', 'AAA'))
self.assertEqual(set(), read.coveredIndices())
def testCoverageOfOneTrigPoint(self):
"""
If a scanned read has one trig point, its coveredIndices method must
return the index of that trig point.
"""
read = ScannedRead(AARead('id', 'AAA'))
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual({0}, read.coveredIndices())
def testGetPairsOneLandmark(self):
"""
If a scanned read has one landmark, its getPairs method should generate
no pairs because there is nothing to pair with.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
self.assertEqual([], list(read.getPairs()))
def testCoverageOfOneLandmarkPoint(self):
"""
If a scanned read has one landmark, its coveredIndices method must
return the indices of that landmark.
"""
read = ScannedRead(AARead('id', 'AAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
self.assertEqual({0, 1}, read.coveredIndices())
def testCoverageOfTwoTrigPoints(self):
"""
If a scanned read has two trig points, its coveredIndices method must
return the indices of those trig points.
"""
read = ScannedRead(AARead('id', 'AAA'))
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
trigPoint = TrigPoint('name', 'symbol', 1)
read.trigPoints.append(trigPoint)
self.assertEqual({0, 1}, read.coveredIndices())
def testCoverageOfTwoIdenticalTrigPoints(self):
"""
If a scanned read has two trig points that occur at the same index, its
coveredIndices method must return the common index of the trig point.
"""
read = ScannedRead(AARead('id', 'AAA'))
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual({0}, read.coveredIndices())
def testGetPairsOneLandmarkOneTrigPointLimitZero(self):
"""
If a scanned read has one landmark and one trig point, but getPairs
is given a limit of 0, no pairs should be generated.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual([], list(read.getPairs(limitPerLandmark=0)))
def testGetPairsOneLandmarkOneTrigPoint(self):
"""
If a scanned read has one landmark and one trig point, its getPairs
method should generate one pair.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual([(landmark, trigPoint)], list(read.getPairs()))
def testCoverageOfTwoDifferentOverlappingLandmarkPoints(self):
"""
If a scanned read has two landmarks, its coveredIndices method must
return the indices of those two landmarks.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol1', 0, 5)
read.landmarks.append(landmark)
landmark = Landmark('name', 'symbol2', 4, 2)
read.landmarks.append(landmark)
self.assertEqual({0, 1, 2, 3, 4, 5}, read.coveredIndices())
def testGetPairsOneLandmarkTwoTrigPoints(self):
"""
If a scanned read has one landmark and two trig points, its getPairs
method should generate two pairs.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
trigPoint1 = TrigPoint('name', 'symbol', 1)
trigPoint2 = TrigPoint('name', 'symbol', 2)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs())
self.assertEqual([(landmark, trigPoint1), (landmark, trigPoint2)],
result)
def testGetPairsTwoLandmarksTwoTrigPointsMinDistanceThree(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate one pair if a minimum distance of 3 is
passed and three trig points are too close.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs(minDistance=5))
self.assertEqual([(landmark1, trigPoint2)], result)
def testReadIsStored(self):
"""
A scanned read must store the read it is passed.
"""
read = AARead('id', 'AAA')
scannedRead = ScannedRead(read)
self.assertIs(read, scannedRead.read)
def testAddTrigPoint(self):
"""
It must be possible to add a trig point to a scanned read.
"""
read = ScannedRead(AARead('id', 'AAA'))
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertIs(trigPoint, read.trigPoints[0])
def testPrintDescription(self):
"""
Check that the print_ method of a scanned read produces the
expected result when given a description.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
expected = ('Query: id\n'
' Length: 5\n'
' Covered indices: 5 (100.00%)\n'
' Landmark count 2, trig point count 2')
self.assertEqual(expected, read.print_(description='Query'))
def testAddLandmark(self):
"""
It must be possible to add a landmark to a scanned read.
"""
read = ScannedRead(AARead('id', 'AAA'))
landmark = Landmark('name', 'symbol', 0, 1)
read.landmarks.append(landmark)
self.assertIs(landmark, read.landmarks[0])
def testGetPairsTwoLandmarksOneTrigPoint(self):
"""
If a scanned read has two landmarks and one trig point, its getPairs
method should generate four pairs in the correct order of closeness,
not yielding (landmark, landmark) pairs with the second landmark to
the left of the first (i.e., not yielding (landmark2, landmark1)).
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'symbol', 0, 2)
landmark2 = Landmark('name', 'symbol', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint = TrigPoint('name', 'symbol', 4)
read.trigPoints.append(trigPoint)
result = list(read.getPairs())
self.assertEqual(
[(landmark1, landmark2), (landmark1, trigPoint),
(landmark2, trigPoint)],
result)
def testPrintSequence(self):
"""
Check that the print_ method of a scanned read produces the
expected result when requested to print the sequence.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
expected = ('Read: id\n'
' Sequence: AAAAA\n'
' Length: 5\n'
' Covered indices: 5 (100.00%)\n'
' Landmark count 2, trig point count 2')
self.assertEqual(expected, read.print_(printSequence=True))
def testGetPairsTwoLandmarksTwoTrigPointsLimitOne(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate two pairs if a limit of 1 nearby feature per
landmark is passed.
Note that even if limitPerLandmark=1 were not specified, the
(landmark2, landmark1) pair would not be produced since landmark2 is
to the right of landmark1.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 4)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs(limitPerLandmark=1))
self.assertEqual([(landmark1, landmark2), (landmark2, trigPoint1)],
result)
def testGetPairsTwoLandmarksTwoTrigPointsMaxDistanceThree(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate three pairs if a maximum distance of 3 is
passed and one trig point is too far away.
Note that the (landmark2, landmark1) pair is not produced since
landmark2 is to the right of landmark1.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs(maxDistance=3))
self.assertEqual(
[(landmark1, landmark2), (landmark1, trigPoint1),
(landmark2, trigPoint1)],
result)
def testPrintFeatures(self):
"""
Check that the print_ method of a scanned read produces the
expected result when asked to print the read's features.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
expected = ('Read: id\n'
' Length: 5\n'
' Covered indices: 5 (100.00%)\n'
' Landmark count 2, trig point count 2\n'
" name symbol=L1 offset=0 len=2 detail=''\n"
" name symbol=L2 offset=1 len=2 detail=''\n"
' name symbol=T1 offset=3\n'
' name symbol=T2 offset=5')
self.assertEqual(expected, read.print_(printFeatures=True))
def testGetPairsTwoLandmarksTwoTrigPoints(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate six pairs, in the correct order of closeness,
not yielding (landmark, landmark) pairs with the second landmark to
the left of the first until all other pairs have been yielded.
Note that the (landmark2, landmark1) pair is not produced since
landmark2 is to the right of landmark1.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'symbol', 0, 2)
landmark2 = Landmark('name', 'symbol', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'symbol', 4)
trigPoint2 = TrigPoint('name', 'symbol', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs())
self.assertEqual(
[(landmark1, landmark2), (landmark1, trigPoint1),
(landmark1, trigPoint2),
(landmark2, trigPoint1), (landmark2, trigPoint2)],
result)
def testNoLandmarks(self):
"""
A freshly created scanned read must have no landmarks.
"""
read = ScannedRead(AARead('id', 'AAA'))
self.assertEqual(0, len(read.landmarks))
def testNoTrigPoints(self):
"""
A freshly created scanned read must have no trig points.
"""
read = ScannedRead(AARead('id', 'AAA'))
self.assertEqual(0, len(read.trigPoints))